Thanks, I will look into this.
--Lilla
On Mon, 15 Nov 2010, Joakim Vinberg wrote:
Lilla,
Terrific! Here is the trace file.
Best,
Joakim
-----Original Message----- From: Lilla Zollei [mailto:lzollei@nmr.mgh.harvard.edu] Sent: Monday, November 15, 2010 7:37 AM To: Joakim Vinberg Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] More information about mri_cvs_register
Hi Joakim,
First the follow-up question: We are interested specifically in multi-modal integration with CVS. In particular, we are curious about functional data in specific sub-cortical regions. Would applyMorph be able to morph a functional overlay volume (.nii file?)
Yes. It can read nifti files and as long as the file that you are morphing is in the same space as the data that you used for registration, you should be fine. If you are morphing a lable map, just make sure to use the nearest neighbor interpolation.
Second, we have been testing mri_cvs_register and have received the
same
error in all of our attempts. I've reproduced a lot of the last lines from the error message below, as well as attached the log. Do these indicate an error I can easily correct? Thanks again for all of the help!
Can you send me the "trace" file from your output directory? That would be more helpful for debugging?
Lilla
before reading annotation /home/decharms/data/freesurfer/round4/9033b/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/free surfer/average/colortable_desikan_killiany.txt) trying to write annotation /usr/local/freesurfer/bin /home/decharms/data/freesurfer/cvs_test perl /usr/local/freesurfer//bin/elastic_registration_CVS.pl --fixed 9032b --moving 903 3b --settings /usr/local/freesurfer//bin/mri_cvs_register.settings.txt --exe surf2vol
--pial
settings: /home/decharms/data/freesurfer/round4
===================== settings: aparc.annot ======================== ===================== settings: norm ======================== ===================== processing brain 9033b ======================== ===================== template brain 9032b ======================== trying to execute elastic registration -> cmd line = surf2vol -fixed_mri /home/decharms/data/freesurfer/round4/9032b/mri/norm.mgz -moving _mri /home/decharms/data/freesurfer/round4/9033b/mri/norm.mgz -fixed_surf /home/decha rms/data/freesurfer/round4/9032b/surf/lh.white -moving_surf /home/decharms/data/free surfer/round4/9033b/cvs/lh.resample.white -fixed_surf_2 /home/decharms/data/freesurfer /round4/9032b/surf/rh.white -moving_surf_2 /home/decharms/data/freesurfer/round4/9033b /cvs/rh.resample.white -fixed_surf_3 /home/decharms/data/freesurfer/round4/9032b/sur f/lh.pial -moving_surf_3 /home/decharms/data/freesurfer/round4/9033b/cvs/lh.resample.p ial -fixed_surf_4 /home/decharms/data/freesurfer/round4/9032b/surf/rh.pial -moving_su rf_4 /home/decharms/data/freesurfer/round4/9033b/cvs/rh.resample.pial -aparc /home/d echarms/data/freesurfer/round4/9032b/label/lh.aparc.annot -aparc_2 /home/decharms/data /freesurfer/round4/9032b/label/rh.aparc.annot -aparc_3 /home/decharms/data/freesurfer/ round4/9032b/label/lh.aparc.annot -aparc_4 /home/decharms/data/freesurfer/round4/9032b /label/rh.aparc.annot -lin_res 20 -ksp_rtol 1.0e-9 -cache_transform /home/decharms/dat a/freesurfer/round4/9033b/cvs/transform.txt -penalty_weight 1000 -fem_steps 17 -elt_vo l_range 5.0,10.0 -log_summary -poisson .3 -topology_old -compress -pc_type none -ksp_t ype preonly -pc_type jacobi -ksp_type cg -ksp_view
-ksp_converged_reason
-out /home/de charms/data/freesurfer/round4/9033b/cvs/el_reg_to9032b.mgz -out_surf /home/decharms/da ta/freesurfer/round4/9033b/cvs/surf-mfc_to9032b -out_mesh /home/decharms/data/freesurf er/round4/9033b/cvs/el_reg_to9032b &> /home/decharms/data/freesurfer/round4/9033b/cvs/ trace_el_reg_to9032b_9033b.txt error executing surf2vol at /usr/local/freesurfer//bin/elastic_registration_CVS.pl lin e 162.
-----Original Message----- From: Lilla Zollei [mailto:lzollei@nmr.mgh.harvard.edu] Sent: Friday, November 12, 2010 12:25 PM To: Joakim Vinberg Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] More information about mri_cvs_register
Hi Joakim,
I had a couple of questions regarding mri_cvs_register (which looks terrific), and couldn't find any answers after a quick search. If I missed an important page or pages, please don't hesitate to send me there.
We are interested in using mri_cvs_register on a large body of
subjects.
Specifically, I am curious if we should choose a single subject to be the template for this analysis, or whether we can use the fsaverage brain as the template?
You will not be able to use fsaverage as a template as it does not
have
a corresponding surface and volumetric atlas. We are in the process of building and releasing a CVS atlas, but it is not ready yet, so for
now
the best thing to do would be to register all your subjects to a randomly selected one.
Second, approximately how long can we expect mri_cvs_register to take for a single CVS alignment? We're running a quad-core Athlon Phenom
with
4GB total; mri_cvs_register is getting a single core (ish) in this
case?
The longest step at the moment is the volumetric registration which might take about 15 hrs. The rest is about 2 hours.
Yes, it is going to get a single core except when it is reading in and writing the non-linear registration warp. Then it might go up to even
I am working on changing this as it causes a bit of a bottleneck.
Finally, what does the output of this function look like? Can we use
it
with the typical transform processes, or are their dedicated
functions
to use after the alignment?
"mri_cvs_register --help" gives you the full list of out put files. basically, you will end up with some registered volumes and a set of non-linear warps. The full CVS warp is currently not saved as it takes up a lot of memory. If you want to construct it and apply it to a new volume, you would need to call two functions:
(1) createMorph --out fullCVSmorph.tm3d --template template.mgz \ --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph el_reg_toTEMPLATE.tm3d
(2) applyMorph --template template.mgz --transform fullCVSmorph.tm3d \ vol movingvol.mgz outputvol.mgz linear
I will add these and more details to the wiki, but please let me know
if
you have any more questions.
--Lilla
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